- Research article
- Open Access
Profile of whole blood gene expression following immune stimulation in a wild passerine
© Meitern et al.; licensee BioMed Central Ltd. 2014
- Received: 8 April 2014
- Accepted: 24 June 2014
- Published: 27 June 2014
Immunoecology aims to explain variation among hosts in the strength and efficacy of immunological defences in natural populations. This requires development of biomarkers of the activation of the immune system so that they can be collected non-lethally and sampled from small amounts of easily obtainable tissue. We used transcriptome profiling in wild greenfinches (Carduelis chloris) to detect whole blood transcripts that most profoundly indicate upregulation of antimicrobial defences during acute phase response. The more general aim of this study was to obtain a functional annotation of a substantial portion of the greenfinch transcriptome that would enable to gain access to more specific genomic tools in subsequent studies. The birds received either bacterial lipopolysaccharide or saline injections and RNA-seq transcriptional profiling was performed 12 h after treatment to provide initial functional annotation of the transcriptome and assess whole blood response to immune stimulation.
A total of 66,084 transcripts were obtained from de novo Trinty assembly, out of which 23,153 could be functionally annotated. Only 1,911 of these were significantly upregulated or downregulated. The manipulation caused marked upregulation of several transcripts related to immune activation. These included avian-specific antimicrobial agents avidin and gallinacin, but also some more general host response genes, such as serum amyloid A protein, lymphocyte antigen 75 and copper-transporting ATPase 1. However, links with avian immunity for most differentially regulated transcripts remained rather hypothetical, as a large set of differentially expressed transcripts lacked functional annotation.
This appears to be the first large scale transcriptional profiling of immune function in passerine birds. The transcriptomic data obtained suggest novel markers for the assessment of the immunological state of wild passerines. Characterizing the function of those possible novel infection markers would assist future vertebrate genome annotation. The extensive sequence information collected enables to identify possible target and housekeeping genes needed to gain access to more specific genomic tools in future studies.
- Gene Ontology
- Zebra Finch
- Acute Phase Response
- Chicken Genome
- Immune Stimulation
Parasites and pathogens are recognized as a major evolutionary force, and all living organisms face a continual struggle to fend off immunological insults within their environment reviewed in [1, 2]. A host’s ability to resist infection is therefore often seen as a major determinant of fitness in nature . Yet most of our knowledge about the function and dynamics of immune responses comes from laboratory studies of inbred mice in highly controlled environments with limited exposure to infection. Natural populations, on the other hand, exhibit wide genetic and environmental diversity . Immunoecology links patterns of immune responses and disease susceptibility to individual fitness consequences [5–7], and asks how immune defences have evolved, are used and are optimized in different environments, ecological settings and lineages. Integrating genomic information into immunoecological research enables to see how variation in genetic background can be linked to phenotypic variation, allowing insight into genetic architecture of protective immune phenotypes [4, 8]. However, wild vertebrate species with well-understood ecology typically lack genome sequences . To obtain species-specific nucleotide sequences without prohibitive costs and time required for sequencing of a complete genome, gene expression data can be used . Transcriptome data provides direct insight into the functional part of the genome, enabling one to study the genetic basis of phenotypic variation in species that lack reference sequences . Consequently, sequencing the normalized mRNA pools of various non-model organisms has become increasingly popular amongst researchers ([11–15] and references therein).
While greater discovery of rare transcripts can be made by sequencing normalized mRNA pools, sequencing non-normalized samples enables one to obtain valuable information about changes in gene expression . Nevertheless, experiments looking at large scale transcriptional changes in ecological studies are generally restricted to species for which microarrays could be developed [16, 17]. However, obtaining data of gene expression via sequencing rather than using specific microarray hybridization would not only allow detection of novel transcripts and retrieve species-specific data, but would reduce bias in gene expression profiling from possible cross-species hybridization mismatches [16, 18, 19].
Immunoecological studies generally require non-invasive markers to allow longitudinal sampling from small amount of easily obtainable tissue . Hence characterizing gene expression of blood cells seems to be the choice in this field. So far, the majority of studies that have looked at transcriptional changes following an experimentally induced immune challenge in live animals have focused on a few transcripts that are well known to be associated with an immune response [20–24]. However, few of these studies have highlighted large numbers of genes not specifically involved in immune function [17, 25, 26]. Characterizing the full transcriptional profile following an immune challenge would thus facilitate the design of novel and more accurate primers for genes related to immune system activation.
The study species greenfinch, Carduelis chloris, is an extensively studied gregarious seed-eating passerine of the Palearctic region that diverged from zebra finches, the closest species with an assembled genome, ~25 MY ago . Plumage coloration of greenfinches is sexually selected  and sensitive to infections [29–31]. Greenfinches tolerate captivity well , which facilitates research in ecophysiology, e.g. , immune function [34, 35], chronic infections [36, 37], oxidative stress , behaviour  and personality . Currently there is no greenfinch gene expression data in the NCBI nucleotide database. However, such data are required for selecting appropriate qPCR control and target genes in studies of gene expression. Adding transcriptome data to current information about the physiology and ecology of greenfinches would thus facilitate further immunoecological research on this avian model.
We have compared transcriptome expression in immune-challenged vs sham-injected greenfinches 12 h after injection with bacterial lipopolysaccharides (LPS) to see which genes were expressed in the blood during the acute phase response (APR). LPS is a part of the cell wall of gram-negative bacteria, which are universally present in most environments. A challenge with LPS mimics a functionally relevant natural situation. Injection of LPS initiates APR by mimicking the first stages of a bacterial infection without actually resulting in sustained disease reviewed in . The APR has become an important tool in examining the effects of immune activation on the performance and functionality of other condition-dependent life-history traits reviewed in . It constitutes energetically the most expensive part of an immune response , characterized by hyperthermia, the release of endogenous proinflammatory cytokines, the release of glucocorticoids and the presentation of sickness behaviour reviewed in . Specifically, we aimed to (i) obtain a functional annotation of a substantial portion of the greenfinch transcriptome, and (ii) identify transcripts significantly upregulated or downregulated in the blood following an immune challenge.
Female wild greenfinches were captured in mist-nets at bird feeders in a garden in the city of Tartu, Estonia (58°22′ N, 26°43′ E) on 7th, 8th, 14th and 15th January 2013. The birds were housed indoors in individual cages (27 × 51 × 55 cm) with sand-covered floors in a single room where they could see their neighbours. The average temperature in the aviary during the experiment was 13.4 ± 1.3°C (average values are given with ± standard deviation). The birds were supplied ad libitum with sunflower seeds and tap water, and were exposed to a natural day-length cycle using artificial lighting by luminophore tubes. They were released back to their natural habitat on 14th March 2013. The study was conducted under license from the Estonian Ministry of the Environment (Licence # 1–4.1/11/100, issued on 23rd March 2011), and the experiment was approved by the Committee of Animal Experiments at the Estonian Ministry of Agriculture (decision # 95, issued on 17th January 2012).
To assess the RNA expression of experimental groups, the reads from each sample were mapped to the assembled transcriptome. Treatment groups were compared by Baggerly's test , which calculates the proportion of counts in a group of samples against those of another group, and is suitable for cases where replicates are available in the groups. In the data, a positive fold change indicates upregulation following immune challenge. Expression difference was calculated for all of the contigs. Expression levels presented refer to RPKM (Reads Per Kilobase of transcript per Million mapped reads) separately for both treatment groups.
De novo assembly resulted in 66,084 sequences with a total length of 39.3 million and mean length of 596 bp (N50 = 803, N25 = 1678). The longest and shortest sequences assembled were 13,752 and 201 bp, respectively. Twelve sequences from this dataset were omitted after passing the sequences through NCBI TSA submission contamination screen, on suspicion of bacterial contamination. Around a third of the resulting assembled contigs were successfully annotated using Uniprot-SwissProt (23,151 annotations) with an average identity of 69 ± 21% (the full list of annotated transcripts is given in Additional file 1: Table S1). Only 11,936 of these were unique genes. Setting the e-value to 1E-20 reduced this number to 7,135 (average identity 84 ± 13%, average coverage 43 ± 35%). NCBI nr database enabled to annotate a similar number (24,553) of contigs with an average identity of 81 ± 23%. Altogether, ~44% (28,925) of the assembled contigs found a hit from one or both of the abovementioned databases.
As anticipated, the highest expression was detected for different hemoglobin subunits which made up more than a third from the total unique gene reads per individual. Other highly expressed transcripts (RPKM >1000) included ferritin, histone H5, carbonic anhydrase and RNAs coding various ribosomal proteins, but also included three unannotated transcripts.
Most significant differentially regulated transcripts
LPS ± SD
Saline ± SD
Known or possible functions
Gallinacin-2 (Beta-defensin 2)
4.7 ± 2.3
0.02 ± 0.03
12.3 ± 5
0.2 ± 0.3
Serum amyloid A protein
16.1 ± 8.3
0.6 ± 0.3
183 ± 76.8
24.1 ± 28.8
leukocyte chemoattractant, oxidant scavenging, antimicrobial activity
DnaJ (Hsp40) homolog, subfamily C 12
10.4 ± 5.7
4.5 ± 2.4
co-chaperone for Hsp70 proteins 
Ruby-eye protein 2
13.5 ± 6.2
6 ± 1.4
eumelanin synthesis 
Lymphocyte antigen 75 (C-type lectin, CD205)
62.9 ± 23.2
29.8 ± 12.1
General transcription factor IIH subunit 1
69.8 ± 32.9
33.8 ± 7.9
part of DNA repair complex TFIIH 
ADP/ATP translocase 3 (ANT3)
67.6 ± 15.7
32.9 ± 8
cellular energy metabolism, mediation of T-cell survival 
Copper-transporting ATPase 1
10.6 ± 1.6
5.1 ± 1.3
regulation of macrophage function and extracellular superoxide dismutase activity 
Down syndrome critical region protein
25.9 ± 2.7
12.9 ± 1.3
part of polymeric immunoglobulin receptor transporter retromere complex
Sodium-coupled neutral amino acid transporter 2 (SNAT2)
19.3 ± 7.9
49.1 ± 9.5
cell volume regulation, response to osmotic stress or amino acid depletion 
This greenfinch gene expression data enabled us to identify possible target and housekeeping genes needed to access to more specific genomic tools in subsequent studies. Although the results incorporate a high number of unreliably annotated sequences, evaluating CEGs from the dataset suggest nearly complete transcriptome coverage. The highly expressed sequences for which no match was found could represent non-coding RNAs that cannot be identified. Even in mammals, a large part of regulatory RNAs is still unidentified , so that ~40% of reads map to unannotated regions . Considering also the general bias towards mammalian annotations in public databases, the annotation of only 1/3 of the assembled transcripts is not surprising. Mapping our assembly to zebra finch cDNA database showed similar coverage. Moreover, the majority of transcripts easily mapped to the zebra finch genome, whereas mapping to the chicken genome was rather poor. This discrepancy may reflect differences in phylogenetic distance between the species, as reducing word size improved mapping to the chicken genome. However, problems in short read data assembly are also well known . Therefore reliable annotations could be expected primarily for highly expressed sequences.
Differential expression data showed the transcripts most strongly affected by immune stimulation. To our knowledge, this kind of large scale profiling of immune function has not been done previously on greenfinches or any other passerines. Similarly to immune stimulation of zebrafish (Danio rerio) embryos , a large proportion (~70%) of differentially expressed sequences lacked a functional annotation, even when only those with higher expression levels were considered. These unannotated transcripts may represent novel immune response genes in birds that need to be checked for this function in subsequent studies.
Although the differentially regulated annotated transcripts with reasonably high expression levels could be tied to immune response or related processes (Table 1), in some cases their exact source and participation in avian immunity remains unclear. This applies especially to the vps26 family protein, DSCR3. Upregulation of mammalian vps26 promotes transcytosis of polymeric immunoglobulin receptor – polymeric immunoglobulin A complex in epithelial cells . However, its upregulation following an in vivo immune challenge has not been previously reported. LPS-induced regulation of HPS5 is quite intriguing. HPS5 (Ruby eye-2) is an ubiquitously expressed protein in vivo related to melanocyte differentiation and eumelanin synthesis . Its absence influences the distribution of CD63 , the platelet activation antigen essential for leukocyte recruitment . Hence, upregulation of HPS5 during the greenfinch immune response suggests the genes involvement in linking melanin-based traits and immune function – a concept proposed in vertebrates . However, the pleiotropic effect of HPS5 in the avian model systems remains to be established.
Upregulation of a conserved transcription initiation factor TFIIH core subunit, GTFIIH1 (p62), as well as the downregulation of SLC38A2 could reflect a global change in cell functioning. Differential expression of SLC38A2 is expected following enhanced proteolysis that causes an increase in transporter substrate amino acids known to inhibit the transcription of SLC38A2  and upregulation of p62 promotes increased transcription by binding to thyroid hormone receptors . Nevertheless, upregulation of the superoxide dismutase activity modulator, ATP7A , suggests the need for improved DNA damage repair in response to increased oxidative insult, so that induced expression of the whole TFIIH complex cannot be ruled out (p62 might induce recruitment of other parts of this DNA repair complex ). The differential regulation of DNAJC12 may also reflect general transcriptional changes by maintaining the molecular function of estrogen receptors together with HSP70 . Although none of the annotated HSP70 transcripts were upregulated, stress-induced increase in the activity of some HSP70s is achieved by regulating the corresponding HSP40 levels .
The upregulation of SLC25A6 could be expected due to its role in promoting Th cell survival . Immunomodulatory role of protein M126 is an expected finding, considering that other members of S100 calgranulin family proteins have known antimicrobial anti-inflammatory roles  and the protein is upregulated in chicken cecum after bacterial infection . Similarly, upregulation of GAL2, AVID, SAA and LY75 can be expected, based on some avian immune stimulation studies [53, 61, 78] and our general knowledge about the functions of these proteins reviewed in [55–57, 62]. However the roles of AVID and SAA in avian immunity remain unclear, supposedly together having an anti-inflammatory role by suppressing cell proliferation and supplying host cells with nutrients [53, 79]. Indeed, for several other upregulated transcripts or their protein family members, an anti-inflammatory role has been suggested (M126, i.e. S100 calcgranulins , GAL2 i.e. beta-defencins , HPS5 , DSCR3 i.e. vps26 retromer complex ). These findings suggest that 12 h after immunostimulation, anti-inflammatory proteins already dominate at the transcriptomic level. However, while upregulation of M126, GAL2 and LY75 in avian leukocytes is expected, the transcriptional upregulation of SAA and AVID in whole blood suggest that the immune response-related transcriptional upregulation of these common acute-phase proteins in the tissue can be detected. Previously the leukocyte upregulation of SAA following an immune response has been found in human blood . Our results indicate that sauropsid whole blood mRNA sampling also has a diagnostic value in immunoecological studies of small vertebrates, where obtaining sufficient amount of blood for isolating leukocytes is not possible without terminal sampling.
The relative lack of shared genes with human common host response  compares favourably with more recent microarray studies involving in vivo immune stimulation of gilthead seabream (Sparus aurata) skeletal muscle cells, human alveolar macrophages  and leukocytes . These studies show regulation of some INF, IL, tumour necrosis factor (TNF) and TLRs, but share only a few upregulated transcripts with our data. Similarly, comparing the list of 420 differentially expressed transcripts with 63 differentially regulated genes identified in a microarray analysis involving LPS administration of chicken liver, muscle and intestinal tissues  indicated 3 shared transcripts – IL8, Gallinacin (GAL) and epidermal growth factor receptor (EGFR), although 36 of them were present in the total dataset. While variations in sampling time and quantification methods contribute to these differences, the presence of some low copy-number host response genes could have been masked by the abundance of hemoglobin and other high copy-number erythrocyte transcripts. Moreover, significant inter-host variation in transcript abundance may have masked upregulation of common host response genes as over half of the human common host response genes were present in our dataset with no significant upregulation. Nevertheless, several differentially regulated transcripts have been linked to the immune response of vertebrates and birds, in particular. This, together with the considerable loss of body mass among LPS-injected birds confirms successful immune system stimulation and immune responsive nature of upregulated transcripts in our experiment.
The excess of erythrocyte transcripts in our data allows us to consider their participation in the immune response, as suggested from some in vitro studies [23, 84]. In most vertebrate species the principal component of blood, erythrocytes, are nucleated, expressing proteins and mRNAs related to various physiological processes other than oxygen transport . Although it has been long known that non-nucleated erythrocytes participate in an immune response , the issue is not well studied . Only recently it has been suggested that chicken red blood cells upregulate toll-like receptor 3 (TLR3), type I interferon's (IFN) and IL8 transcripts in response to viral dsRNA mimetic poly I:C [23, 84]. In rainbow trout (Oncorhynchus mykiss) erythrocytes, both heat stress and in vitro incubation with LPS modulate genes related to stress, immune response, apoptosis and hematopoiesis [85, 87]. Although upregulation of IL8 coincides with induced expression in chicken erythrocytes by poly I:C , no common transcripts with in vitro LPS stimulated rainbow trout erythrocytes  could be detected. Our data thus suggest that the role of nucleated erythrocytes in LPS-induced immune response in vivo is small. Comparison with other tissues is necessary to consolidate this conclusion.
Finally, we were unable to determine the extent to which differences in transcriptome expression between LPS- and saline-injected birds can be ascribed to endotoxin-induced changes in leukocyte numbers. LPS injection usually causes transient changes in the concentration of different types of circulating leukocytes . In domestic chicken, the number of circulating heterophils correlates with mRNA expression of different inflammatory cytokines and chemokines at different time intervals subsequent to corticosterone administration . The question as to whether and how differential gene expression relates to the profile the cellular composition of the blood in non-model species needs to be addressed, preferably correlating within-individual changes in gene expression with corresponding changes in circulating leukocyte counts. Another limitation of our study is that the birds were sampled only at one time-point of the APR, which means that we could have missed other differentially expressed transcripts that appear before and after the 12 h time-point of sampling. Such issues can be addressed by multiple time-point measurements in future studies. Preferably along with increased sequencing depth.
In passerines, detecting upregulation of antimicrobial defences during acute phase response can be achieved by quantifying whole blood mRNA of SAA, AVID, M126 or GAL2. Quantifying these transcripts along with a selection of housekeeping genes, should provide reliable biomarkers to estimate immune system activation from small blood samples, i.e., in situations where non-terminal sampling is required and only small amounts of tissue can be collected. We also provide the first transcriptome sequencing data of greenfinches, facilitating integration of genomic tools into research involving this species.
Availability of supporting data
The data sets supporting the results of this article are included within the article and its additional file and available in the DDBJ/EMBL/GenBank under the accession GBCG00000000 (http://www.ncbi.nlm.nih.gov/nuccore/GBCG00000000).
We thank Tuul Sepp, Ulvi Karu, Marju Männiste, and Mari-Ann Lind for help with bird maintenance, experiments and biochemical analyses. Two anonymous reviewers provided constructive criticism on the ms. The study was financed by the Estonian Ministry of Education and Science (target-financing project # 0180004 s09) and by the European Union through the European Regional Development Fund (Centre of Excellence FIBIR). RA was supported by SF0180026s09 from the Estonian Ministry of Education and Research and by the EU ERDF through the Estonian Centre of Excellence in Genomics.
- Schmid-Hempel P: Evolutionary Parasitology. The Integrated Study of Infections, Immunology, Ecology, and Genetics. 2011, New York: Oxford University PressGoogle Scholar
- Wilson K, Cotter SC: Host-parasite interactions and the evolution of immune defense. Adv Study Behav. 2013, 45: 81-174.View ArticleGoogle Scholar
- Jackson JA, Begon M, Birtles R, Paterson S, Friberg IM, Hall A, Ralli C, Turner A, Zawadzka M, Bradley JE: The analysis of immunological profiles in wild animals: a case study on immunodynamics in the field vole, Microtus agrestis. Mol Ecol. 2011, 20 (5): 893-909.PubMedView ArticleGoogle Scholar
- Pedersen AB, Babayan SA: Wild immunology. Mol Ecol. 2011, 20 (5): 872-880.PubMedView ArticleGoogle Scholar
- Demas GE, Nelson RJ: Ecoimmunology. 2011, New York: Oxford University PressGoogle Scholar
- Schulenburg H, Kurtz J, Moret Y, Siva-Jothy MT: Introduction. Ecological immunology. Philos Trans R Soc B: Biol Sci. 2009, 364: 3-14.View ArticleGoogle Scholar
- Sheldon BC, Verhulst S: Ecological immunology: costly parasite defences and trade-offs in evolutionary ecology. Trends Ecol Evol. 1996, 11: 317-321.PubMedView ArticleGoogle Scholar
- Ellegren H, Sheldon BC: Genetic basis of fitness differences in natural populations. Nature. 2008, 452 (7184): 169-175.PubMedView ArticleGoogle Scholar
- Peterson M, Whittaker D, Ambreth S, Sureshchandra S, Buechlein A, Podicheti R, Choi J-H, Lai Z, Mockatis K, Colbourne J, Tang H, Ketterson E: De novo transcriptome sequencing in a songbird, the dark-eyed junco (Junco hyemalis): genomic tools for an ecological model system. BMC Genomics. 2012, 13 (1): 305-PubMed CentralPubMedView ArticleGoogle Scholar
- Bouck A, Vision T: The molecular ecologist's guide to expressed sequence tags. Mol Ecol. 2007, 16 (5): 907-924.PubMedView ArticleGoogle Scholar
- Künstner A, Wolf JBW, Backström N, Whitney O, Balakrishnan CN, Day L, Edwards SV, Janes DE, Schlinger BA, Wilson RK, Jarvis ED, Warren WC, Ellegren H: Comparative genomics based on massive parallel transcriptome sequencing reveals patterns of substitution and selection across 10 bird species. Mol Ecol. 2010, 19 (SUPPL. 1): 266-276.PubMed CentralPubMedView ArticleGoogle Scholar
- Feldmeyer B, Wheat CW, Krezdorn N, Rotter B, Pfenninger M: Short read Illumina data for the de novo assembly of a non-model snail species transcriptome (Radix balthica, Basommatophora, Pulmonata), and a comparison of assembler performance. BMC Genomics. 2011, 12 (1): 317-PubMed CentralPubMedView ArticleGoogle Scholar
- Santure AW, Gratten J, Mossman JA, Sheldon BC, Slate J: Characterisation of the transcriptome of a wild great tit Parus major population by next generation sequencing. BMC Genomics. 2011, 12: 283-PubMed CentralPubMedView ArticleGoogle Scholar
- Srivastava A, Winker K, Shaw TI, Jones KL, Glenn TC: Transcriptome analysis of a North American songbird, melospiza melodia. DNA Res. 2012, 19 (4): 325-333.PubMed CentralPubMedView ArticleGoogle Scholar
- Subramanian S, Huynen L, Millar CD, Lambert DM: Next generation sequencing and analysis of a conserved transcriptome of New Zealand's kiwi. BMC Evol Biol. 2010, 10 (1): 387-PubMed CentralPubMedView ArticleGoogle Scholar
- Wang Z, Gerstein M, Snyder M: RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet. 2009, 10 (1): 57-63.PubMed CentralPubMedView ArticleGoogle Scholar
- Webster LMI, Paterson S, Mougeot F, Martinez-Padilla J, Piertney SB: Transcriptomic response of red grouse to gastro-intestinal nematode parasites and testosterone: implications for population dynamics. Mol Ecol. 2011, 20 (5): 920-931.PubMedView ArticleGoogle Scholar
- Oshlack A, Chabot AE, Smyth GK, Gilad Y: Using DNA microarrays to study gene expression in closely related species. Bioinformatics. 2007, 23 (10): 1235-1242.PubMedView ArticleGoogle Scholar
- Whitehead A, Crawford DL: Variation within and among species in gene expression: raw material for evolution. Mol Ecol. 2006, 15 (5): 1197-1211.PubMedView ArticleGoogle Scholar
- Kaitetzidou E, Crespo D, Vraskou Y, Antonopoulou E, Planas JV: Transcriptomic Response of Skeletal Muscle to Lipopolysaccharide in the Gilthead Seabream (Sparus aurata). Mar Biotechnol. 2012, 14 (5): 605-619.PubMedView ArticleGoogle Scholar
- Martin LB, Kidd L, Liebl AL, Coon CAC: Captivity induces hyper-inflammation in the house sparrow (Passer domesticus). J Exp Biol. 2011, 214 (15): 2579-2585.PubMedView ArticleGoogle Scholar
- Naidu KS, Morgan LW, Bailey MJ: Inflammation in the avian spleen: timing is everything. BMC Mol Biol. 2010, 11 (1): 104-PubMed CentralPubMedView ArticleGoogle Scholar
- St Paul M, Paolucci S, Barjesteh N, Wood RD, Sharif S: Chicken erythrocytes respond to Toll-like receptor ligands by up-regulating cytokine transcripts. Res Vet Sci. 2013, 95 (1): 87-91.PubMedView ArticleGoogle Scholar
- Vinkler M, Svobodová J, Gabrielová B, Bainová H, Bryjová A: Cytokine expression in phytohaemagglutinin-induced skin inflammation in a galliform bird. J Avian Biol. 2014, 45: 43-50.View ArticleGoogle Scholar
- Bonneaud C, Balenger SL, Russell AF, Zhang J, Hill GE, Edwards SV: Rapid evolution of disease resistance is accompanied by functional changes in gene expression in a wild bird. Proc Natl Acad Sci. 2011, 108 (19): 7866-7871.PubMed CentralPubMedView ArticleGoogle Scholar
- Pemberton J, Beraldi D, Craig B, Hopkins J: Digital gene expression analysis of gastrointestinal helminth resistance in Scottish blackface lambs. Mol Ecol. 2011, 20 (5): 910-919.PubMedView ArticleGoogle Scholar
- Barker FK, Cibois A, Schikler P, Feinstein J, Cracraft J: Phylogeny and diversification of the largest avian radiation. Proc Natl Acad Sci U S A. 2004, 101 (30): 11040-11045.PubMed CentralPubMedView ArticleGoogle Scholar
- Eley C: Status Signalling In The Western Greenfinch (Carduelis chloris). PhD thesis. 1991, Brighton: University of SussexGoogle Scholar
- Lindström K, Lundström J: Male greenfinches (Carduelis chloris) with brighter ornaments have higher virus infection clearance rate. Behav Ecol Sociobiol. 2000, 48: 44-51.View ArticleGoogle Scholar
- Männiste M, Hõrak P: Emerging infectious disease selects for darker plumage coloration in greenfinches. Front Ecol Evol. 2014, 2: 4-View ArticleGoogle Scholar
- Merilä J, Sheldon BC, Lindström K: Plumage brightness in relation to haematozoan infections in the greenfinch Carduelis chloris : Bright males are a good bet. Ecoscience. 1999, 6 (1): 12-18.Google Scholar
- Sepp T, Sild E, Hõrak P: Hematological Condition Indexes in Greenfinches: Effects of Captivity and Diurnal Variation. Physiol Biochem Zool. 2010, 83 (2): 276-282.PubMedView ArticleGoogle Scholar
- Peters A, Delhey K, Andersson S, van Noordwijk H, Forschler MI: Condition-dependence of multiple carotenoid-based plumage traits: an experimental study. Funct Ecol. 2008, 22: 831-839.View ArticleGoogle Scholar
- Aguilera E, Amat J: Carotenoids, immune response and the expression of sexual ornaments in male greenfinches (Carduelis chloris). Naturwissenschaften. 2007, 94: 895-902.PubMedView ArticleGoogle Scholar
- Sarv T, Hõrak P: Phytohaemagglutinin injection has a long-lasting effect on immune cells. J Avian Biol. 2009, 40 (5): 569-571.View ArticleGoogle Scholar
- Lindström K, Krakower D, Lundström JO, Silverin B: The effects of testosterone on a viral infection in greenfinches (Carduelis chloris): an experimental test of the immunocompetence-handicap hypothesis. Proc R Soc Lond Ser B Biol Sci. 2001, 268: 207-211.View ArticleGoogle Scholar
- Sepp T, Karu U, Blount JD, Sild E, Männiste M, Hõrak P: Coccidian Infection Causes Oxidative Damage in Greenfinches. PLoS ONE. 2012, 7 (5): e36495-PubMed CentralPubMedView ArticleGoogle Scholar
- Meitern R, Sild E, Kilk K, Porosk R, Hõrak P: On the methodological limitations of detecting oxidative stress: effects of paraquat on measures of oxidative status in greenfinches. J Exp Biol. 2013, 216 (14): 2713-2721.PubMedView ArticleGoogle Scholar
- Lilliendahl K: Daily accumulation of body reserves under increased predation risk in captive Greenfinches Carduelis chloris. Ibis. 2000, 142: 587-595.View ArticleGoogle Scholar
- Herborn KA, Coffey J, Larcombe SD, Alexander L, Arnold KE: Oxidative profile varies with personality in European greenfinches. J Exp Biol. 2011, 214 (10): 1732-1739.PubMedView ArticleGoogle Scholar
- Hegemann A, Matson KD, Versteegh MA, Villegas A, Tieleman BI: Immune response to an endotoxin challenge involves multiple immune parameters and is consistent among the annual-cycle stages of a free-living temperate zone bird. J Exp Biol. 2013, 216 (14): 2573-2580.PubMedView ArticleGoogle Scholar
- King MO, Swanson DL: Activation of the immune system incurs energetic costs but has no effect on the thermogenic performance of house sparrows during acute cold challenge. J Exp Biol. 2012, 216 (11): 2097-2102.View ArticleGoogle Scholar
- Iseri VJ, Klasing KC: Dynamics of the systemic components of the chicken (Gallus gallus domesticus) immune system following activation by Escherichia coli; implications for the costs of immunity. Dev Comp Immunol. 2013, 40 (3–4): 248-257.PubMedView ArticleGoogle Scholar
- Meitern R, Sild E, Lind M-A, Männiste M, Sepp T, Karu U, Hõrak P: Effects of Endotoxin and Psychological Stress on Redox Physiology, Immunity and Feather Corticosterone in Greenfinches. PLoS ONE. 2013, 8 (6): e67545-PubMed CentralPubMedView ArticleGoogle Scholar
- Chiari Y, Galtier N: RNA extraction from sauropsids blood: evaluation and improvement of methods. Amphibia-Reptilia. 2011, 32 (1): 136-139.View ArticleGoogle Scholar
- Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q: Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol. 2011, 29 (7): 644-652.PubMed CentralPubMedView ArticleGoogle Scholar
- Zhao Y, Tang H, Ye Y: RAPSearch2: a fast and memory-efficient protein similarity search tool for next-generation sequencing data. Bioinformatics. 2012, 28 (1): 125-126.PubMed CentralPubMedView ArticleGoogle Scholar
- McCarthy FM, Bridges SM, Wang N, Magee GB, Williams WP, Luthe DS, Burgess SC: AgBase: A unified resource for functional analysis in agriculture. Nucleic Acids Res. 2007, 35 (SUPPL. 1): D599-D603.PubMed CentralPubMedView ArticleGoogle Scholar
- Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ: Basic local alignment search tool. J Mol Biol. 1990, 215 (3): 403-410.PubMedView ArticleGoogle Scholar
- Parra G, Bradnam K, Korf I: CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes. Bioinformatics. 2007, 23 (9): 1061-1067.PubMedView ArticleGoogle Scholar
- Jenner RG, Young RA: Insights into host responses against pathogens from transcriptional profiling. Nat Rev Microbiol. 2005, 3 (4): 281-294.PubMedView ArticleGoogle Scholar
- Baggerly KA, Deng L, Morris JS, Aldaz CM: Differential expression in SAGE: accounting for normal between-library variation. Bioinformatics. 2003, 19 (12): 1477-1483.PubMedView ArticleGoogle Scholar
- Matulova M, Rajova J, Vlasatikova L, Volf J, Stepanova H, Havlickova H, Sisak F, Rychlik I: Characterization of Chicken Spleen Transcriptome after Infection with Salmonella enterica Serovar Enteritidis. PLoS ONE. 2012, 7 (10): e48101-PubMed CentralPubMedView ArticleGoogle Scholar
- Matulova M, Varmuzova K, Sisak F, Havlickova H, Babak V, Stejskal K, Zdrahal Z, Rychlik I: Chicken innate immune response to oral infection with Salmonella enterica serovar Enteritidis. Vet Res. 2013, 44 (1): 37-PubMed CentralPubMedView ArticleGoogle Scholar
- Cuperus T, Coorens M, van Dijk A, Haagsman HP: Avian host defense peptides. Dev Comp Immunol. 2013, 41 (3): 352-369.PubMedView ArticleGoogle Scholar
- Tuohimaa P, Joensuu T, Isola J, Keinänen R, Kunnas T, Niemelä A, Pekki A, Wallén M, Ylikomi T, Kulomaa M: Development of progestin-specific response in the chicken oviduct. Int J Dev Biol. 1989, 33 (1): 125-134.PubMedGoogle Scholar
- Uhlar CM, Whitehead AS: Serum amyloid A, the major vertebrate acute-phase reactant. Eur J Biochem. 1999, 265 (2): 501-523.PubMedView ArticleGoogle Scholar
- Hsu K, Champaiboon C, Guenther BD, Sorenson BS, Khammanivong A, Ross KF, Geczy CL, Herzberg MC: Anti-infective protective properties of S100 calgranulins. Anti-Inflammatory Anti-Allergy Agents Med Chem. 2009, 8 (4): 290-305.View ArticleGoogle Scholar
- Qiu XB, Shao YM, Miao S, Wang L: The diversity of the DnaJ/Hsp40 family, the crucial partners for Hsp70 chaperones. Cell Mol Life Sci. 2006, 63 (22): 2560-2570.PubMedView ArticleGoogle Scholar
- Hirobe T, Wakamatsu K, Ito S: A new mutation of mouse ruby-eye 2, ru2d/hps5 ru2-d inhibits eumelanin synthesis but stimulates pheomelanin synthesis in melanocytes. Zool Sci. 2012, 29 (10): 652-661.PubMedView ArticleGoogle Scholar
- Staines K, Young JR, Butter C: Expression of Chicken DEC205 Reflects the Unique Structure and Function of the Avian Immune System. PLoS ONE. 2013, 8 (1): e51799-PubMed CentralPubMedView ArticleGoogle Scholar
- Figdor CG, Van Kooyk Y, Adema GJ: C-type lectin receptors on dendritic cells and langerhans cells. Nat Rev Immunol. 2002, 2 (2): 77-84.PubMedView ArticleGoogle Scholar
- Compe E, Egly JM: TFIIH: When transcription met DNA repair. Nat Rev Mol Cell Biol. 2012, 13 (6): 343-354.PubMedView ArticleGoogle Scholar
- Jang J-Y, Lee C-E: IL-4-induced upregulation of adenine nucleotide translocase 3 and its role in Th cell survival from apoptosis. Cell Immunol. 2006, 241 (1): 14-25.PubMedView ArticleGoogle Scholar
- Kim HW, Chan Q, Afton SE, Caruso JA, Lai B, Weintraub NL, Qin Z: Human macrophage ATP7A is localized in the trans-Golgi apparatus, controls intracellular copper levels, and mediates macrophage responses to dermal wounds. Inflammation. 2012, 35 (1): 167-175.PubMed CentralPubMedView ArticleGoogle Scholar
- Vergés M, Luton F, Gruber C, Tiemann F, Reinders LG, Huang L, Burlingame AL, Haft CR, Mostov KE: The mammalian retromer regulates transcytosis of the polymeric immunoglobulin receptor. Nat Cell Biol. 2004, 6 (8): 763-769.PubMedView ArticleGoogle Scholar
- Franchi-Gazzola R, Dall'Asta V, Sala R, Visigalli R, Bevilacqua E, Gaccioli F, Gazzola GC, Bussolati O: The role of the neutral amino acid transporter SNAT2 in cell volume regulation. Acta Physiol. 2006, 187 (1–2): 273-283.View ArticleGoogle Scholar
- McGettigan PA: Transcriptomics in the RNA-seq era. Curr Opin Chem Biol. 2013, 17 (1): 4-11.PubMedView ArticleGoogle Scholar
- Schatz MC, Delcher AL, Salzberg SL: Assembly of large genomes using second-generation sequencing. Genome Res. 2010, 20 (9): 1165-1173.PubMed CentralPubMedView ArticleGoogle Scholar
- Stockhammer OW, Zakrzewska A, Hegedûs Z, Spaink HP, Meijer AH: Transcriptome profiling and functional analyses of the zebrafish embryonic innate immune response to salmonella infection. J Immunol. 2009, 182 (9): 5641-5653.PubMedView ArticleGoogle Scholar
- Wei ML: Hermansky-Pudlak syndrome: a disease of protein trafficking and organelle function. Pigment Cell Res. 2006, 19 (1): 19-42.PubMedView ArticleGoogle Scholar
- Huizing M, Hess R, Dorward H, Claassen DA, Helip-Wooley A, Kleta R, Kaiser-Kupfer MI, White JG, Gahl WA: Cellular, molecular and clinical characterization of patients with Hermansky-Pudlak syndrome type 5. Traffic. 2004, 5 (9): 711-722.PubMedView ArticleGoogle Scholar
- Doyle EL, Ridger V, Ferraro F, Turmaine M, Saftig P, Cutler DF: CD63 is an essential cofactor to leukocyte recruitment by endothelial P-selectin. Blood. 2011, 118 (15): 4265-4273.PubMedView ArticleGoogle Scholar
- Ducrest AL, Keller L, Roulin A: Pleiotropy in the melanocortin system, coloration and behavioural syndromes. Trends Ecol Evol. 2008, 23 (9): 502-510.PubMedView ArticleGoogle Scholar
- Hyde R, Cwiklinski EL, MacAulay K, Taylor PM, Hundal HS: Distinct Sensor Pathways in the Hierarchical Control of SNAT2, a Putative Amino Acid Transceptor, by Amino Acid Availability. J Biol Chem. 2007, 282 (27): 19788-19798.PubMedView ArticleGoogle Scholar
- Liu Y, Ando S, Xia X, Yao R, Kim M, Fondell J, Yen PM: p62, a TFIIH subunit, directly interacts with thyroid hormone receptor and enhances T3-mediated transcription. Mol Endocrinol. 2005, 19 (4): 879-884.PubMedView ArticleGoogle Scholar
- Terada K, Yomogida K, Imai T, Kiyonari H, Takeda N, Kadomatsu T, Yano M, Aizawa S, Mori M: A type I DnaJ homolog, DjA1, regulates androgen receptor signaling and spermatogenesis. EMBO J. 2005, 24 (3): 611-622.PubMed CentralPubMedView ArticleGoogle Scholar
- Kunnas TA, Wallén MJ, Kulomaa MS: Induction of chicken avidin and related mRNAs after bacterial infection. Biochim Biophys Acta(BBA)-Gene Struct Expr. 1993, 1216 (3): 441-445.View ArticleGoogle Scholar
- Zerega B, Pagano A, Pianezzi A, Ulivi V, Camardella L, Cancedda R, Cancedda FD: Expression of Serum Amyloid A in chondrocytes and myoblasts differentiation and inflammation: Possible role in cholesterol homeostasis. Matrix Biol. 2004, 23 (1): 35-46.PubMedView ArticleGoogle Scholar
- Zhou B, Yun EY, Ray L, You J, Ip YT, Lin X: Retromer promotes immune quiescence by suppressing Spätzle-Toll pathway in Drosophila. J Cell Physiol. 2014, 229 (4): 512-520.PubMed CentralPubMedView ArticleGoogle Scholar
- Talwar S, Munson PJ, Barb J, Fiuza C, Cintron AP, Logun C, Tropea M, Khan S, Reda D, Shelhamer JH, Danner RL, Suffredini AF: Gene expression profiles of peripheral blood leukocytes after endotoxin challenge in humans. Physiol Genomics. 2006, 25 (2): 203-215.PubMedView ArticleGoogle Scholar
- Reynier F, de Vos AF, Hoogerwerf JJ, Bresser P, van der Zee JS, Paye M, Pachot A, Mougin B, van der Poll T: Gene expression profiles in alveolar macrophages induced by lipopolysaccharide in humans. Mol Med. 2012, 18 (9): 1303-1311.PubMed CentralPubMedView ArticleGoogle Scholar
- Baurhoo B, Ferket P, Ashwell CM, de Oliviera J, Zhao X: Cell walls of Saccharomyces cerevisiae differentially modulated innate immunity and glucose metabolism during late systemic inflammation. PLoS ONE. 2012, 7 (1): e30323-PubMed CentralPubMedView ArticleGoogle Scholar
- Morera D, Roher N, Ribas L, Balasch JC, Doñate C, Callol A, Boltaña S, Roberts S, Goetz G, Goetz FW: RNA-seq reveals an integrated immune response in nucleated erythrocytes. PLoS ONE. 2011, 6 (10): e26998-PubMed CentralPubMedView ArticleGoogle Scholar
- Morera D, MacKenzie SA: Is there a direct role for erythrocytes in the immune response. Vet Res. 2011, 42: 89-PubMed CentralPubMedView ArticleGoogle Scholar
- Siegel I, Lin Liu T, Gleicher N: The red-cell immune system. Lancet. 1981, 318 (8246): 556-559.View ArticleGoogle Scholar
- Lewis JM, Hori TS, Rise ML, Walsh PJ, Currie S: Transcriptome responses to heat stress in the nucleated red blood cells of the rainbow trout (Oncorhynchus mykiss). Physiol Genomics. 2010, 42 (3): 361-373.PubMedView ArticleGoogle Scholar
- Wang W, Wideman RF, Chapman ME, Bersi TK, Erf GF: Effect of intravenous endotoxin on blood cell profiles of broilers housed in cages and floor litter environments. Poult Sci. 2003, 82 (12): 1886-1897.PubMedView ArticleGoogle Scholar
- Shini S, Shini A, Kaiser P: Cytokine and chemokine gene expression profiles in heterophils from chickens treated with corticosterone. Stress Int J Biol Stress. 2010, 13 (3): 185-194.View ArticleGoogle Scholar
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